The impact of anthropogenic climate change, particularly felt in the most vulnerable regions in the South, such as Sub-Saharan Africa, induces changes in contemporary migration patterns. Although there is no consensus whether migration is a consequence of climate change, an adaptive strategy to climate change or both, either way there is a strong interference with human health. The confluence of climate change and migration aggravates health vulnerabilities and results in health problems requiring priority attention. Besides the moral obligation of responding to these health problems, as entrenched in the 2030 Sustainable Development Goals Agenda, several international legal instruments protect the human rights of all people, hence the right to health of migrants. Building resilient health systems is a precondition to better support the changing health needs due to migration. Nonetheless, there is a lack of resilience frameworks for health systems in the context of climate change and migration in Sub-Saharan Africa. These frameworks should entail components about climate change resilience but also migrant-inclusiveness is necessary to strengthen health systems. Therefore, this study aims to develop a strategic framework, building upon evidence from a scoping review, and qualitative data from a case study. The case study will represent a specific country where primary care professionals are interviewed for their central role in the local health system and the community. This approach will allow to build a resilience framework that is flexible for contextual adaptation and practical use in fragile regions of Sub-Saharan Africa.